Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome Leonardo Arbiza1, Joaquı´n Dopazo2, Herna´n Dopazo1* 1 Pharmacogenomics and Comparative Genomics Unit, Centro de Investigacio´nPrı´ncipe Felipe (CIPF), Valencia, Spain, 2 Functional Genomics Unit, Bioinformatics Department, Centro de Investigacio´nPrı´ncipe Felipe (CIPF), Valencia, Spain For years evolutionary biologists have been interested in searching for the genetic bases underlying humanness. Recent efforts at a large or a complete genomic scale have been conducted to search for positively selected genes in human and in chimp. However, recently developed methods allowing for a more sensitive and controlled approach in the detection of positive selection can be employed. Here, using 13,198 genes, we have deduced the sets of genes involved in rate acceleration, positive selection, and relaxation of selective constraints in human, in chimp, and in their ancestral lineage since the divergence from murids. Significant deviations from the strict molecular clock were observed in 469 human and in 651 chimp genes. The more stringent branch-site test of positive selection detected 108 human and 577 chimp positively selected genes. An important proportion of the positively selected genes did not show a significant acceleration in rates, and similarly, many of the accelerated genes did not show significant signals of positive selection. Functional differentiation of genes under rate acceleration, positive selection, and relaxation was not statistically significant between human and chimp with the exception of terms related to G-protein coupled receptors and sensory perception. Both of these were over-represented under relaxation in human in relation to chimp. Comparing differences between derived and ancestral lineages, a more conspicuous change in trends seems to have favored positive selection in the human lineage. Since most of the positively selected genes are different under the same functional categories between these species, we suggest that the individual roles of the alternative positively selected genes may be an important factor underlying biological differences between these species. Citation: Arbiza L, Dopazo J, Dopazo H (2006) Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput Biol 2(4): e38. DOI: 10.1371/journal.pcbi.0020038 Introduction fully sequenced species. In a recent work, Dorus et al. [9] found significantly higher rates of gene evolution in the For years evolutionary biologists have been interested in primate nervous system when comparing against house- knowing to what extent natural selection and genetic drift keeping and among subsets of brain-specific genes. From have shaped the genetic variation of populations and species this data they proposed natural selection as the underlying [1–5]. Neutrality tests have provided powerful tools for mechanism. Other efforts have focused on finding direct developing hypotheses regarding this issue. The first objective molecular evidence of PS. Clark et al. [10], using more than of related studies had been to make general inferences about 7,600 homologous sequences, found 1,547 human and 1,534 the causes of molecular evolution, and many efforts have chimp genes as likely candidates to have been acted upon by been made to search for deviations from the molecular clock PS. In a later study, Nielsen et al. [11], using more than 13,000 hypothesis. However, in the past ten years the focus has changed toward finding molecular events showing positive selection (PS) [6]. Editor: David Hillis, University of Texas, United States of America PS is the process favoring the retention in a population of Received September 21, 2005; Accepted March 15, 2006; Published April 28, 2006 those mutations that are beneficial to the reproductive A previous version of this article appeared as an Early Online Release on March 15, success of individuals. Contrary to this process, the molecular 2006 (DOI: 10.1371/journal.pcbi.0020038.eor). clock hypothesis [7,8] postulates that the rate of evolution of DOI: 10.1371/journal.pcbi.0020038 molecular sequences is roughly constant over time. This Copyright: Ó 2006 Arbiza et al. This is an open-access article distributed under the observation has been taken as a strong evidence for the terms of the Creative Commons Attribution License, which permits unrestricted neutral mutation hypothesis [3], which postulates that the use, distribution, and reproduction in any medium, provided the original author majority of molecular changes in evolution are due to neutral and source are credited. or nearly neutral mutations [2]. With the growing framework Abbreviations: AH-PSG, PSG in the ancestral hominid lineage; CDS, coding sequences; ChF, chimp faster than human; Ch-PSG, chimp PSG; CSAC, Chimpanzee available for comparative genomic studies, it has been Sequencing and Analysis Consortium; GO, gene ontology; HF, human faster than possible to test for neutrality against positive (or negative) chimp; H-PSG, human PSG; Ka, nonsynonymous rate of evolution in substitutions selection at a genomic level. per site; Ka-RRT, relative rates test on nonsynonymous sites; K–S, Kolmogorov– Smirnov; Ks, synonymous rate of evolution in substitutions per site; ML, maximum- Recent efforts at a large or genomic scale have been likelihood; PS, positive selection; PSG, positively selected genes; Q, quadrant; RRT, conducted to elucidate the intricacies of human evolution by relative rates test; RSC, relaxation of selective constraints means of comparing rate differences and PS against other * To whom correspondence should be addressed. E-mail: [email protected] PLoS Computational Biology | www.ploscompbiol.org0288 April 2006 | Volume 2 | Issue 4 | e38 Adaptive Evolution in Hominids Synopsis employing corrections for multiple testing as the norm for all comparisons, while considering the uncorrected sets for Since the publication of the human and the chimp genomes, one of confirmation of specific results where appropriate. the major challenges in evolutionary biology has begun to be Therefore many important questions regarding the iden- deciphered: namely, the search for positively selected genes that tity and functional roles of genes showing acceleration, RSC, have shaped humanness. Arbiza and colleagues undertake a and PS, still remain: which are the genes that can be assigned genomic-scale search for the genes that have been positively to these sets with a considerable degree of sensitivity and selected in human, in chimp, and in their common ancestral lineage. confidence? Are these genes significantly different between They conclude that events of positive selection were six times more frequent in chimp than in human, although they do not group species in functional terms? Do these genes encompass a under specific functional classes that have been preferentially special group of functional classes, or are they an unbiased selected in either species. However, in the comparisons of the representation of the genome? To what extent do the set of evolutionary trends between the ancestral and the descendant positively selected genes (PSG) differ from the set of lineages, they found that most of the relative differences in common accelerated genes? How many of the PSG can be distinguished classes show an abundance of positive selection on the human from cases of RSC? Furthermore, can we gain any additional branch. By differentiating positive selection from a relaxation of insight by comparing the pattern of adaptation of the derived selective constraints, both producing analogous footprints in the species against that in their ancestral lineage? genome, they demonstrate that many of the genes previously All of these questions can only be answered by testing for thought to have been positively selected correspond to likely cases of relaxation. Finally, they quantify the bias produced by the use of deviations from the neutral theory in human, in chimp, and average rate–based approaches to concentrate cases of adaptive in their common ancestor, independently, using sensitive evolution in these species. tests for PS while correcting for multiple testing. In this study, we have searched for the most complete set of known human genes with the chimp, mouse, rat, and dog orthologs available orthologous sequences, found that 733 genes deviated from in order to answer all of these questions. strict neutrality, showing evidences of PS. In the latest The two branch-site maximum likelihood (ML) tests of PS genomic study published as of the time of this writing, the employed in this paper benefit from a high degree of Chimpanzee Sequencing and Analysis Consortium (CSAC) sensitivity when compared with previous branch tests, and found 585 out of 13,454 human–chimp orthologous genes as can be used together, as has been recently shown [14], in an potential candidates to have been acted upon by PS, showing approach that allows detecting lineage-specific events while a Ka/Ki . 1 [12]. distinguishing true cases of PS from likely cases of RSC. Both Indeed, while these three publications have been hallmarks these tests are based on the comparison of the likelihood with in the genomic-scale search for events showing PS and have which two alternative models fit sequence data. Test I provided much insight into the subject, the combination of compares the nearly neutral null model (M1a) against the methods used have produced certain disagreements and have alternative PS model (A). M1a assumes two codon site classes evolving under purifying selection and neutral evolution in left some important considerations unaccounted for. As all the lineages of the phylogeny. Model A considers two noted in the CSAC publication, the set of 585 genes observed additional site classes conserved or evolving neutrally on all may only be enriched for cases of PS given that, for example, the branches (background lineages), except on a specified the Ka/Ki statistic used could be .1 by chance in almost half branch where PS is tested for (the foreground lineage). Test II of these genes if purifying selection is allowed to act non compares the null model (A1) against the alternative model A.